A comparative analysis of proteomic maps of long-term grown and fresh clinical Trichomonas vaginalis isolates exhibiting low and high virulence phenotypes, respectively, was performed using two-dimensional gel electrophoresis and mass spectrometry. Of 29 protein spots differentially expressed between the isolates, 19 were over-expressed in the isolate exhibiting high virulence phenotype: proteins associated with cytoskeletal dynamics, such as coronin and several isoforms of actin, as well as proteins involved in signal transduction, protein turnover, proteolysis, and energetic and polyamine metabolisms were identified. Some malate dehydrogenase, fructose-1,6-bisphosphate aldolase and ornithine cyclodeamidase isoforms were exclusively expressed by the highly virulent isolate. During interaction assays with VEC, parasites exhibiting high virulence phenotype rapidly adhered and switched to amoeboid forms. In contrast, low adhesion and no morphological transformation were observed in parasites displaying low virulence phenotype. Our findings demonstrate that expression of specific proteins by high and low virulence parasites could be associated with the ability of each isolate to undergo morphological transformation and interact with host cells. Such data represent an important step towards understanding of the complex interaction network of proteins that participate in the mechanism of pathogenesis of this protozoan.